FindMyFriends-package	FindMyFriends-package
.fillDefaults	fillDefaults
.loadPgExample	loadPgExample
addGenomes	addGenomes
addGenomes,pgVirtual,pgVirtual-method	addGenomes
addGroupInfo	addGroupInfo
addGroupInfo,pgVirtual-method	addGroupInfo
addOrgInfo	addOrgInfo
addOrgInfo,pgVirtual-method	addOrgInfo
as	pgVirtual-class
cdhitGrouping	cdhitGrouping
cdhitGrouping,pgVirtual-method	cdhitGrouping
collapseParalogues	collapseParalogues
collapseParalogues,pgVirtual-method	collapseParalogues
defaults	defaults
defaults,pgVirtual-method	defaults
defaults<-	defaults
defaults<-,pgVirtual-method	defaults
geneLocation	geneLocation
geneLocation,pgInMemLoc-method	geneLocation
geneNames	geneNames
geneNames,pgFull-method	geneNames
geneNames,pgLM-method	geneNames
geneNames,pgSlim-method	geneNames
geneNames<-	geneNames
geneNames<-,pgFull-method	geneNames
geneNames<-,pgLM-method	geneNames
geneNames<-,pgSlim-method	geneNames
genes	genes
genes,pgFull,character-method	genes
genes,pgFull,missing-method	genes
genes,pgLM,character-method	genes
genes,pgLM,missing-method	genes
genes,pgSlim,character-method	genes
genes,pgSlim,missing-method	genes
geneWidth	geneWidth
geneWidth,pgFull-method	geneWidth
geneWidth,pgLM-method	geneWidth
geneWidth,pgSlim-method	geneWidth
getNeighborhood	getNeighborhood
getNeighborhood,pgVirtualLoc-method	getNeighborhood
getRep	getRep
getRep,pgVirtual,character-method	getRep
gpcGrouping	gpcGrouping
gpcGrouping,pgVirtual-method	gpcGrouping
graphGrouping	graphGrouping
graphGrouping,pgVirtual-method	graphGrouping
groupGenes	internalGroupGenes
groupGenes,pgInMem-method	internalGroupGenes
groupGenes,pgVirtual-method	internalGroupGenes
groupInfo	groupInfo
groupInfo,pgInMem-method	groupInfo
groupInfo<-	groupInfo
groupInfo<-,pgInMem-method	groupInfo
groupNames	groupNames
groupNames,pgInMem-method	groupNames
groupNames<-	groupNames
groupNames<-,pgInMem-method	groupNames
groupStat	groupStat
groupStat,pgVirtual-method	groupStat
hasGeneGroups	hasGeneGroups
hasGeneGroups,pgVirtual-method	hasGeneGroups
hasGeneInfo	hasGeneInfo
hasGeneInfo,pgVirtual-method	hasGeneInfo
hasParalogueLinks	hasParalogueLinks
hasParalogueLinks,pgVirtual-method	hasParalogueLinks
internal-groupGenes	internalGroupGenes
internal-mergePangenomes	internalMergePangenomes
internal-metadata	internalMetadata
kmerLink	kmerLink
kmerLink,pgVirtual-method	kmerLink
kmerSimilarity	kmerSimilarity
kmerSimilarity,pgVirtual-method	kmerSimilarity
kmerSplit	kmerSplit
kmerSplit,pgVirtual-method	kmerSplit
length,pgVirtual-method	pgVirtual-class
manualGrouping	manualGrouping
manualGrouping,pgVirtual,integer-method	manualGrouping
manualGrouping,pgVirtual,list-method	manualGrouping
mergePangenomes	internalMergePangenomes
mergePangenomes,pgFull,pgFull-method	internalMergePangenomes
mergePangenomes,pgFullLoc,pgFullLoc-method	internalMergePangenomes
mergePangenomes,pgInMem,pgInMem-method	internalMergePangenomes
mergePangenomes,pgLM,pgLM-method	internalMergePangenomes
mergePangenomes,pgLMLoc,pgLMLoc-method	internalMergePangenomes
mergePangenomes,pgSlimLoc,pgSlimLoc-method	internalMergePangenomes
neighborhoodSplit	neighborhoodSplit
neighborhoodSplit,pgVirtualLoc-method	neighborhoodSplit
nGeneGroups	nGeneGroups
nGeneGroups,pgVirtual-method	nGeneGroups
nGenes	nGenes
nGenes,pgVirtual-method	nGenes
nOrganisms	nOrganisms
nOrganisms,pgVirtual-method	nOrganisms
orgInfo	orgInfo
orgInfo,pgInMem-method	orgInfo
orgInfo<-	orgInfo
orgInfo<-,pgInMem-method	orgInfo
orgNames	orgNames
orgNames,pgInMem-method	orgNames
orgNames<-	orgNames
orgNames<-,pgInMem-method	orgNames
orgStat	orgStat
orgStat,pgVirtual-method	orgStat
pangenome	pangenome
pcGraph	pcGraph
pcGraph,pgVirtualLoc-method	pcGraph
pgFull-class	pgFull-class
pgFullLoc-class	pgFullLoc-class
pgInMem-class	pgInMem-class
pgInMemLoc-class	pgInMemLoc-class
pgLM-class	pgLM-class
pgLMLoc-class	pgLMLoc-class
pgMatrix	pgMatrix
pgMatrix,pgVirtual-method	pgMatrix
pgSlim-class	pgSlim-class
pgSlimLoc-class	pgSlimLoc-class
pgVirtual-class	pgVirtual-class
pgVirtualLoc-class	pgVirtualLoc-class
plotEvolution	plotEvolution
plotEvolution,pgVirtual-method	plotEvolution
plotGroup	plotGroup
plotGroup,pgVirtual-method	plotGroup
plotNeighborhood	plotNeighborhood
plotNeighborhood,pgVirtualLoc-method	plotNeighborhood
plotSimilarity	plotSimilarity
plotSimilarity,pgVirtual-method	plotSimilarity
plotStat	plotStat
plotStat,pgVirtual-method	plotStat
plotTree	plotTree
plotTree,pgVirtual-method	plotTree
readAnnot	readAnnot
removeGene	removeGene
removeGene,pgInMem,missing,missing,missing,numeric-method	removeGene
removeGene,pgVirtual,character,character,missing,missing-method	removeGene
removeGene,pgVirtual,character,missing,missing,missing-method	removeGene
removeGene,pgVirtual,character,numeric,missing,missing-method	removeGene
removeGene,pgVirtual,missing,character,missing,missing-method	removeGene
removeGene,pgVirtual,missing,character,missing,numeric-method	removeGene
removeGene,pgVirtual,missing,missing,character,missing-method	removeGene
removeGene,pgVirtual,missing,missing,character,numeric-method	removeGene
removeGene,pgVirtual,missing,missing,numeric,missing-method	removeGene
removeGene,pgVirtual,missing,missing,numeric,numeric-method	removeGene
removeGene,pgVirtual,missing,numeric,missing,missing-method	removeGene
removeGene,pgVirtual,missing,numeric,missing,numeric-method	removeGene
reportGroupChanges	reportGroupChanges
seqToGeneGroup	seqToGeneGroup
seqToGeneGroup,pgInMem-method	seqToGeneGroup
seqToOrg	seqToOrg
seqToOrg,pgInMem-method	seqToOrg
setGroupInfo	internalMetadata
setGroupInfo,pgInMem-method	internalMetadata
setOrgInfo	internalMetadata
setOrgInfo,pgInMem-method	internalMetadata
show,pgVirtual-method	pgVirtual-class
translated	translated
translated,pgVirtual-method	translated
variableRegions	variableRegions
variableRegions,pgVirtualLoc-method	variableRegions
[,pgVirtual,character,ANY,ANY-method	pgVirtual-class
[,pgVirtual,integer,ANY,ANY-method	pgVirtual-class
[,pgVirtual,logical,ANY,ANY-method	pgVirtual-class
[,pgVirtual,numeric,ANY,ANY-method	pgVirtual-class
[[,pgVirtual,ANY,ANY-method	pgVirtual-class
